Not OP: but working on a downstream project and my current boss used to work on EMBL-bank in the day. A lot of this stuff is in databases. e.g. Oracle and I th

Not OP: but working on a downstream project and my current boss used to work on EMBL-bank in the day. A lot of this stuff is in databases. e.g. Oracle and I think for advanced search it was in Teradata. However, databases are hard to share so many steps require dumping the database into some interchange formats (custom and often from before the age of XML or JSON, yeah for ASN.1 parsing!) Sharing database dumps is done but commercial licenses and version mismatches do add issues here as well. Remember EMBL/ENA is older than MySQL. The databases tend to have the wrong shape for the next downstream step i.e. table design is related to work flow and if your next step in working is completely different we end up with issues. Also some data can't be published until a certain date so that needs to be filtered from the dumps in some way. Consider as well that this project is 3 decades old and used to be printed in books at some point, and shipped on DVD as recently as 2004. File based operations can be extremely efficient.